[med-svn] [ensembl] branch master created (now 6a04764)

Wed Nov 15 09:49:42 UTC 2017

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository ensembl.

        at  6a04764   Moved packaging from SVN to Git

This branch includes the following new commits:

       new  0ce1274   Initial work on an Ensembl package.
       new  e15d4df   Docs and deps for Ensembl.
       new  6b2ae6e   Got postinst commands done.
       new  dd77b31   First of many patches to get Ensembl to actually _work_
       new  76d1ccb   Patches and config changes to ensembl that will hopefully make it launch first time.
       new  ff86a2f   Some further writing, fix of dependencies.
       new  3c0ee21   Further work towards ensembl.
       new  2681e37   Preparing for svn-buildpackage
       new  7cc567f   Changed recommends.
       new  187f26a   Added section and dependency on mysql-server ... too obvious to spot :)
       new  60196fa   Added initial watch file, stopping prior to removal.
       new  5a06d74   Roud of updates by Richard ... might actually work now :)
       new  3528504   Fix.
       new  dc3ceb8   Round of updates for the Ensembl package.
       new  bea8203   Further improvements.
       new  48fd0a6   Further split of packages.
       new  f008585   Some more (stupid) fixes.
       new  7fc1c91   Refined and optimised patches for Ensembl web module.
       new  e38de48   bioperl may substitute bioperl1.2.3
       new  4f60b25   Added script to perform the download of upstream sources.
       new  dc3d191   Added developers found in source code to list of developers. This is yet incomplete, though.
       new  09ae71b   Fixed download script.
       new  d903be6   Yet another fix.
       new  95c9937   Adapted for lwp-parallel.
       new  db52206   User editing of apache port and mysql conneciton details in Ensembl install script, plus minor change to dependences and patches and overwrites to tidy up a bit.
       new  3677348   The previous version did no longer work with the latest cvs checkout of release 57 in Ensembl ... weird.
       new  e327792   Fixing boiler template redundancy in changelog.
       new  3bb5ce9   Preparation for debconf
       new  b7afb43   Trying to debconf-ise the Ensembl install process.
       new  1328d25   Creationg of /usr/bin for Ensembl package.
       new  850f2bb   Introduction of configuration file.
       new  4b0aabc   Debconf must be there early.
       new  cb57057   Corrected syntax: no == but =
       new  88f5b75   Making package reconfigurable by moving default config files to /etc/defaults/ensembl as well.
       new  8b8462f   Removed extraneous storage of config values for Ensembl.
       new  5d90f86   Fixes towards separately building the arch-dependent packages.
       new  b2c5361   Added a series of directories - redundant with debian/rules for the moment.
       new  af82690   More fine-tuning.
       new  3f750ed   Series of roundups - postinst still has problems.
       new  68e304f   Fixing == vs = bug
       new  3a41c55   Bumping Debian version of package, more lintian cleanliness.
       new  e0dbf41   More == vs = bashisms resolved.
       new  334e239   Added status message when unrolling new database.
       new  1b2ffc2   Fixed Ensembl SQL.
       new  8175bc9   Wrong variable names in Ensembl postinst.
       new  6b8a9fc   Some formatting.
       new  2b7c67f   More changes towards lintian cleanliness.
       new  998a8e1   Fix to username on MySQL for Ensembl.
       new  b4a256f   Missing / before first var directory in Ensembl init.d
       new  3161a6a   Added libensembl-draw-perl, simplified debian/rules
       new  eb58e29   /usr/share/ensembl/utils/integration/deploy.sh needs a tcsh, don't dare to rename it to deploy.csh for the very moment.
       new  e285150   mysql-server and liblwp-parallel-perl are both needed to get this package beyond post-inst.
       new  0d29ece   Adjusting file permissions
       new  0d4253d   Redirecting the temporal directory.
       new  5f39bb0   Creation of files in /var.
       new  2405797   Maybe the Readme has improved, not sure.
       new  791d7ad   Fixed (hopefully) a bunch of lintian warnings.
       new  0f8d36f   improved on some bork, now also treating PMs
       new  dfa32a4   An update script needs the ksh, review this later.
       new  8d899ea   Further deborkation and upload.
       new  a4d5584   Removed tmp directories.
       new  7a51063   Working more towards lintian cleanliness.
       new  436d7ea   No more lintian errors. 59 warnings, still.
       new  5555a8f   Made changes to make Ensembl install properly (issues with db_get and missing templates, amongst others.)
       new  d0b4efc   Template attempt at Ensembl.
       new  6716b73   Sorry left some comments in postinst for ensembl, now removed.
       new  119bc43   Ensembl init.d improved.
       new  17e8fee   More Ensembl tricks.
       new  18fd7d6   Use passive option for ftp server which increases chances to really get the package
       new  bfbca8b   Make sure MD5sum of orig.tar.gz tarballs will remain the same for different checkouts
       new  e218978   Provide get-orig-source target
       new  5561d6e   mv debian/templates debian/ensembl.templates to tell debhelper in what package it should move the template; be nice to translators and makr template descriptions as translatable; add debian/po directory for template translations
       new  085b73f   Add  dh_installdebconf to debian/roles which finally does the trick to install templates and config into the package
       new  c7153c6   Ensembl init.d
       new  a468458   iFinal Ensembl tweaks, I think it installs now.
       new  c3fec3d   Local changes by Richard left uncommitted, bump of Debian version.
       new  c45c5f2   Extension of writing. Helping lintian.
       new  783ac1e   Removed redundant Ensembl template.
       new  6886936   Upload of version 57-5
       new  fcb352f   That Makefile.PL was annoying. It should not be needed.
       new  e692ea7   Automated source package preparation knows how to delete a series of non-DFSG compliant files.
       new  c44e615   Moving Ensembl to non-free.
       new  ee40276   Changes for new upload.
       new  d60c6d8   Preparations for upload -7.
       new  e8d5495   Updated to Ensembl version62
       new  ae6f395   Not required anymore
       new  b032afa   removed MULTI.ini patch
       new  944dd18   Typos, policy.
       new  9dbdd6d   Introduced W: and I: for status messages.
       new  295da8c   May have fixed a lintian warning.
       new  c329c8a   Uploaded Ensembl to Debian PPA for Lucid.
       new  05560a5   Fixed building with -B for autobuilders
       new  1516820   Nicification and -B indeed only builds the arch-dependent bits.
       new  1d0edd2   Preparation for new version 63 of Ensembl
       new  361faf4   Uploaded version 63 to experimental and Debian Med PPA
       new  156a33e   Introduce trunk as policy suggests
       new  6bbd8b2   Fixed Vcs fields; New upstream release
       new  27fcbde   Fix prepare_ensembl_source_packages.sh
       new  b64fa61   Start fighting lintian problems, forther fixes in get-orig-source
       new  610b448   More dependency fixing
       new  8febfe8   Keep on femoving lintian errors
       new  7a64b43   New upstream version was just released
       new  c63de8f   Move around files using dh_install instead of manual copying
       new  b2384e5   Clean up {pre,post}{inst,rm} scripts from useless comments; drop a hackish call in postinst while keeping proper FIXME notes in case this workaround might be needed definitely to enable caring for the problem more properly
       new  b8e48bb   Suppress noise when changing scripts
       new  5597da2   Bug #645487 is closed by the jalview / jemboss dependency
       new  5a17aeb   Make heavy use of `dh_install --autodest`
       new  5608e52   Do not ship copy of memcached code in binary package
       new  74b229e   FOr security reasons use Debian packaged JavaScript library tinymce
       new  9dcd219   Fix another kind of wrong shebang lines
       new  47bdbad   Five lintian warnings and one warning at build time less ...
       new  588e5ec   Remove unneeded script (according to a hint of Nick James)
       new  d17f216   9 lintian warnings about non-executable scripts less
       new  a00efed   Use more Debian packaged JavaScript libraries instead of Ensembl's copy
       new  e1c1351   drop uncompiled sources in  ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit  from the binary package
       new  d699440   Remove executable flag from *.js filese (fixes another two lintian warnings)
       new  480407b   Fix debconf initilisation
       new  fce3663   Removed useles dh-make template
       new  2b341f2   Remove non-functional scripts in perl/default/das/
       new  e439826   Four lintian warnings less by ficing execute permissions and missing shebang lines
       new  51249d5   Adde lintian override for /tmp usage; do not advertise usage of csh in documentation
       new  bb754fc   Get rid of [t]csh instances inside docs and code
       new  4dd640f   No [t]csh dependency needed any more
       new  33250be   Only one package that contains ksh files
       new  818a95a   Work on some lintian warnings regarding documentation issues
       new  cfe7b60   Commit current state of changes to Ensembl after traveling to Debian Med sprint
       new  92e9801   Normalise packaging
       new  6a04764   Moved packaging from SVN to Git

The 128 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.

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